FunFOLD

Determines ligand binding residues using 3D models of proteins. FunFOLD in based on cutting edge function prediction algorithms. It provides a graphical representation of the ligand-binding site, with predicted ligands and binding site residues highlighted. This tool creates a list of residues from the target sequences that are most likely to bind a ligand, along with a list of putative binding ligands.

FunFOLD citations

(11)

library_books

Normal Modes Expose Active Sites in Enzymes

2016

PLoS Comput Biol

PMCID: 5225006

PMID: 28002427

DOI: 10.1371/journal.pcbi.1005293

[…] developed [–]. Several webservers of ligand binding sites have also been constructed and may be used to infer unknown ligand binding sites based on homology and other attributes such as Pocketome [], FunFold [], scPDB [], IBIS [], Multibind [], fPop [], and FINDSITE []. To date however, no comprehensive study comparing geometry based techniques has been performed.Normal-mode analysis is one of the […]

library_books

Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

2015

Int J Mol Sci

PMCID: 4691145

PMID: 26694353

DOI: 10.3390/ijms161226202

[…] tional annotation. Furthermore, a number of structure-based methods for the prediction of protein–ligand binding sites have incorporated methods for predicting GO and EC terms, including COACH [] and FunFOLD3 [,,] (See ). However, as these methods build 3D models as part of their prediction pipeline, they are somewhat more computationally intensive than the sequence-only methods. The prediction of […]

Hairpins under tension: RNA versus DNA

2015

Nucleic Acids Res

PMCID: 4787782

PMID: 26323319

DOI: 10.1093/nar/gkv860

[…] olution of these probabilities. To obtain the experimental hysteresis distributions, for each molecule the unfolding and folding forces measured are paired to generate all possible hysteresis values (Funfold − Ffold). The obtained values are weighted according to the number of force cycles actually performed on the molecule, and normalized. More details about the building of the histograms are pre […]

[…] in Mb is unknown, we sought to computationally predict the ligand-binding site. There are several methods that may be employed, including Q-site Finder [], SiteHound-web [], COACH [], BioLip [], and FunFOLD2 []. Despite their utility, these methods are challenging to apply to predictions in which the comparator proteins are structurally dissimilar and exhibit high sequence divergence. For instanc […]

[…] ii–iv) other than I27's. Both F
unfold (, top side panel) and ΔL (, right side panel) were broadly distributed, ranging from 30 to 120 pN and from 5 to 120 nm, respectively. The unfolding peak force Funfold and contour length change ΔL showed no correlations since no dominant region can be found in . The relationship between Funfold and ΔL as well as their distributions indicate that within those […]